Habitat structure is thought to be important role on ecological communities, but the compound relationship between habitat area and structure are reciprocal and difficult to separate. Indeed, high structure of habitat contained large area of habitats. In present study, species-area relationship of stream invertebrate assemblages on three complexity and five area levels of artificial substrates were compared. In the comparison of species-area patterns on three complexity substrates, the patterns of high and mid complexity showed higher intercept than low ones without slope differences. However, highest complexity showed lower intercept than middle ones. This result indicated that the influence of habitat structure on stream invertebrate assemblages was independent from scale, while suitable complexity of habitat structure established higher species-area curve.